SEARCH · Engineering Papers

Results for “Network centrality”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Optimal operation of multi-plant steam district heating systems for enhanced efficiency and sustainability

Despite their crucial role in supplying heat and power to universities, industries, and healthcare facilities, many steam-based district heating systems rely on outdated control methods. Among these, multi-central plant districts are particularly challenging due to the complexities of coordinating multiple plants, optimizing load distributions, and managing system downtime. In response, new operational strategies are developed to enhance the efficiency and sustainability of steam districts while utilizing existing resources. These strategies include reducing plant operational pressure without compromising the reliable supply to buildings and optimizing load allocation across multiple plants. The load allocation considers boiler part-load efficiency, runtime, network losses, and building pressure set points, and is compared with traditional multi-boiler controls. To support this exploration, new dynamic Modelica models are developed. In addition, methods to reduce modeling complexities are incorporated, enhancing their suitability for practical applications. A holistic district-wide analysis using a real university case study demonstrates a 4.7% fuel savings by lowering boiler operational pressure from 900 kPa to 600 kPa, along with a 13.3% reduction in condensation losses across the distribution network. Furthermore, the load allocation approach results in a 13.1% reduction in fuel consumption during peak winter periods and 15.3% during shoulder periods, with corresponding decreases in carbon emissions and fuel costs. This approach can also save maintenance costs by reducing the boiler runtime by 49.6%. In conclusion, this research underscores the benefits of retrofitting aging steam district heating systems, offering immediate operational improvements by enhancing efficiency, meeting regulatory compliance, and extending infrastructure lifespans while delaying costly overhauls.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Lyapunov stability of smart inverters using linearized distflow approximation

Fast-acting smart inverters that utilize preset operating conditions to determine real and reactive power injection/consumption can create voltage instabilities (over-voltage, voltage oscillations and more) in an electrical distribution network if set-points are not properly configured. In this work, linear distribution power flow equations and droop-based Volt–Var and Volt–Watt control curves are used to analytically derive a stability criterion using Lyapunov analysis that includes the network operating condition. The methodology is generally applicable for control curves that can be represented as Lipschitz functions. The derived Lipschitz constants account for smart inverter hardware limitations for reactive power generation. A local policy is derived from the stability criterion that allows inverters to adapt their control curves by monitoring only local voltage, thus avoiding centralized control or information sharing with other inverters. The criterion is independent of the internal time-delays of smart inverters. Simulation results for inverters with and without the proposed stabilization technique demonstrate how smart inverters can mitigate voltage oscillations locally and mitigate real and reactive power flow disturbances at the substation under multiple scenarios. The study concludes with illustrations of how the control policy can dampen oscillations caused by solar intermittency and cyberattacks.

42 ENGINEERING↗

DOE OSTI2023

Identification of a carbonic anhydrase–Rubisco complex within the alpha-carboxysome

Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO 2 fixation—Rubisco and carbonic anhydrase—and are the centerpiece of the bacterial CO 2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO 2 by carbonic anhydrase, producing a high CO 2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus . We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Computation-Efficient Algorithm for Distributed Feedback Optimization of Distribution Grids

Feedback-based optimization algorithms use real-time measurements to update the optimal control for the underlying system which may not be fully identified. Recently, we have developed a distributed feedback-based algorithm [1] that avoids the requirement of fast communication between central computing and local actuator/sensor agents. This paper extends the work by greatly reducing the number of copies of variables involved in the distributed feedback-based algorithm, which results in faster convergence and lower communication requirement. The main idea is to leverage the specific structural properties of the admittance matrix for distribution systems with tree network topology. We also show the effectiveness of the proposed algorithm in simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Limited-view Cone Beam CT reconstruction using 3D Patch-based Supervised and Adversarial Learning [Slides]

We present a novel machine learning CNN architecture that can learn from limited data combined appropriately with physics and statistical priors (e.g., forward models and noise models). To address the limited availability of training data we adopt a 3D patch-based approach for our models. Patch-based learning is central to several image reconstruction methods and demands fewer training data than DL approaches, as a single data volume can be broken into several millions of overlapping 3D sub-volumes or patches. This creates a very large number of training sub-volumes from a limited number of overall image volumes. A 3D Generative Adversarial Networks (GAN) is then trained to remove artifacts at the sub-volume level. The combination of a sub-volume-based approach with DL allows us to exploit the richness of the latter in extracting and representing image features, while avoiding risks associated with overfitting due to limited training data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Efficient Scalable Contact Network Generation from Population Data

Modeling the contacts among a population is critical to understanding the dynamics of a disease outbreak. Contact networks, where nodes are individuals and edges are contacts among them, are used to represent these complex individual-level interactions. In this work, we are given the daily activity schedules of an urban population that represent the activity location and time of individuals in a population during a single twenty four hour period over multiple days. Using collocation to determine contact between individuals, our goal is to extract hourly contact networks from large-scale activity data. We improve upon the existing adjacency matrix-based method by implementing our custom sparse matrix multiplication algorithm. Starting with a Python implementation, we achieve a 1600x speed up in the computation with a fast custom designed sparse matrix multiplier algorithm implemented in the C++ language. This work is central to future parallel designs of the problem.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1997

Differential Magnetic Field Shear in an Active Region

The three-dimensional extrapolation of magnetic field lines from a magnetogram obtained at Kitt Peak allows us to understand the global structure of the NOAA active region 6718, as observed in X-rays with the Normal Incidence X-ray Telescope (NIXT) and in Ha with the Multichannel Subtractive Double Pass spectrograph (MSDP) in Meudon on 1991 July 11. This active region was in a quiet stage. Bright X-ray loops connect plages having field strengths of approx. 300 G, while H-alpha fibriles connect penumbrae having strong spot fields to the surrounding network. Small, intense X-ray features in the moat region around a large spot, which could be called X-ray-bright points, are due mainly to the emergence of magnetic flux and merging of these fields with surrounding ones. A set of large-scale, sheared X-ray loops is observed in the central part of the active region. Based on the fit between the observed coronal structure and the field configurations (and assuming a linear force-free field), we propose a differential magnetic field shear model for this active region. The decreasing shear in outer portions of the active region may indicate a continual relaxation of the magnetic field to a lower energy state in the progressively older portions of the AR.

Schmeider, B.↗

NASA NTRS1998

The Influence of Soil Moisture and Wind on Rainfall Distribution and Intensity in Florida

Land surface processes play a key role in water and energy budgets of the hydrological cycle. For example, the distribution of soil moisture will affect sensible and latent heat fluxes, which in turn may dramatically influence the location and intensity of precipitation. However, mean wind conditions also strongly influence the distribution of precipitation. The relative importance of soil moisture and wind on rainfall location and intensity remains uncertain. Here, we examine the influence of soil moisture distribution and wind distribution on precipitation in the Florida peninsula using the 3-D Goddard Cumulus Ensemble (GCE) cloud model Coupled with the Parameterization for Land-Atmosphere-Cloud Exchange (PLACE) land surface model. This study utilizes data collected on 27 July 1991 in central Florida during the Convection and Precipitation Electrification Experiment (CaPE). The idealized numerical experiments consider a block of land (the Florida peninsula) bordered on the east and on the west by ocean. The initial soil moisture distribution is derived from an offline PLACE simulation, and the initial environmental wind profile is determined from the CaPE sounding network. Using the factor separation technique, the precise contribution of soil moisture and wind to rainfall distribution and intensity is determined.

Baker, R. David↗

NASA NTRS2009

NASA Global Precipitation Mission Ground Validation Implementation

The Global Precipitation Mission (GPM; core-satellite launch 2013) will provide Ka/Ku-band dual-frequency precipitation radar (DPR) and accompanying passive microwave radiometer-diagnosed precipitation estimates over a latitude range of 65 N to 65 S. The extended latitudinal domain of GPM coverage combined with requirements to detect (and in the case of liquid, estimate) liquid and frozen precipitation rates for values ranging from several hundred to just a few tenths of a millimeter per hour present new challenges to the development of physically-based satellite precipitation retrieval algorithms. On regional scales select national and international resources such as existing calibrated radar and rain gauge networks can provide basic datasets that enable direct statistical validation of GPM core-satellite reflectivitys and core/constellation rain rate measurements. Near-term planned field campaign involvements include Finland/Baltic Sea (fall 2010; joint CloudSat,GPM, and European study of precipitation in low-altitude melting layers and snowfall in the vicinity of the Helsinki testbed), central Oklahoma (spring 2011; joint with DOE ARM- precipitation retrievals over a mid-latitude continental land surface), and the Great Lakes region (winter 2011-12, snowfall retrieval).

Petersen, Walter A.↗

NASA NTRS2022

KMT-2021-BLG-0171Lb and KMT-2021-BLG-1689Lb: Two Microlensing Planets in the KMTNet High-Cadence Fields With Followup Observations

Follow-up observations of high-magnification gravitational microlensing events can fully exploit their intrinsic sensitivity to detect extrasolar planets, especially those with small mass ratios. To make followup observations more uniform and efficient, we develop a system, HighMagFinder, to automatically alert possible ongoing high-magnification events based on the real-time data from the Korea Microlensing Telescope Network (KMTNet). We started a new phase of follow-up observations with the help of HighMagFinder in 2021. Here we report the discovery of two planets in high-magnification microlensing events, KMT- 2021-BLG-0171 and KMT-2021-BLG-1689, which were identified by the HighMagFinder. We find that both events suffer the ‘central-resonant’ caustic degeneracy. The planet-host mass-ratio is q ∼4.7 × 10 −5 or q ∼2.2 × 10 −5 for KMT-2021-BLG-0171, and q ∼2.5 × 10 −4 or q ∼1.8 × 10 −4 for KMT-2021-BLG-1689. Together with two other events, four cases that suffer such degeneracy have been discovered in the 2021 season alone, indicating that the de generate solutions may have been missed in some previous studies. We also propose a quantitative factor to weight the probability of each solution from the phase space. The resonant interpretations for the two events are disfavoured under this consideration. This factor can be included in future statistical studies to weight degenerate solutions.

Micro gravitational lensing↗

NASA NTRS2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

nitrogen fixation↗

NASA NTRS1998

Potential Mars Surveyor 2001 Landing Sites: Low-Elevation Cratered "Highlands" in Central and Eastern Sinus Meridiani and Near Amenthes Fossae

The main scientific goal for the Mars Surveyor Program 2001 (MSP 01) landed mission is to collect and characterize 91 rock and 13 soil core samples using an integrated instrument suite onboard the Athena Rover. If possible, these samples will be retrieved and returned to Earth via a MSP 05 or MSP 07 mission. Preliminary engineering constraints for the MSP 01 landing site call for a location that lies between 15 S and 30 N, and below about 2 km elevation (based on Viking-era topography). Desirable landing sites for MSP 01 are to be located "in the ancient highlands where the environmental conditions may have been favorable to the preservation of evidence of possible prebiotic or biotic processes including the emergence (and, potentially, the persistence) of life". We interpret this to mean that the desirable sites include those that have evidence of aqueous sediments that might have been deposited during the Noachian and/or Hesperian Epochs of Mars' history. In addition to the search for subaqueous sedimentary deposits, we took into consideration the fact that the rover, Athena, will need to be able to access these materials. Thus, a site where aeolian deflation has occurred might be desirable because it might expose, in situ, layered sedimentary deposits. Deflated areas, of course, might include potential landing hazards in the form of meterscale buttes and mesas (e.g., Christmas Lake Valley, OR), thus careful study of such sites with high resolution images will be required before a decision is made to land. We have been examining three regions that have potential to be considered for MSP 01 landing sites. This work is based on Viking (VIS, IRTM) and Phobos 2 (Termoskan) observations and should be regarded as preliminary because we believe that the final site selection should also be based upon analysis of Mars Global Surveyor observations that help constrain mineralogy (TES) and local geomorphology (MOC, MOLA). (1) Eastern Sinus Meridiani Region (proposed by K. S. Edgett) Sinus Meridiani is a persistent low-albedo (< 0. 16) region on the martian equator that has been recognized for about 400 years. All of Sinus Meridiani is below the 2 km elevation constraint for MSP 01. The region includes cratered highlands, valley networks, aeolian dunes, and possible aqueous sedimentary deposits. The landing site study region is located in the eastern portion of Sinus Meridiani. It is bounded by latitudes 10 S to 2 N, longitudes 355 W to 345 W, and the elevations are mostly 1-2 km. The center of this area contains a medium-albedo (0.19-0.21), relatively smooth-surfaced deposit that was suggested by Rice to be a lacustrine deposit. Several potential landing areas can be suggested within this region. Based on Viking and Phobos 2 data, the favored sites so far are centered at 7.6 S, 346.9 W and 0.8 S, 349 W. Thermal inertias are 3.2-7.0 x 10(exp -3) cal /sq cm s(exp -0.5)/K; and rock abundances are around 2-6%. The site at 7.6 S, 346.9 W is at the southern end of the smooth, medium-albedo unit that might have a lacustrine origin. At this location, numerous channels appear to have drained toward the smooth unit. Viking images from orbit 747A show this area at about 15 m/pixel ground resolution. The images reveal that aeolian deflation has occurred along the deposit's margins. Bright (i.e., albedo >= 0.21) aeolian dunes are present on the channel floors and in some of the depressions on the smooth unit. The bright, apparently active dunes might consist of material (perhaps lakedeposited sands) that has been eroded from the smooth unit. The site at approximately 0.8 S, 349 W is selected because it offers an opportunity to solve a long-standing puzzle about Mars remote sensing. There are three main "color" units on Mars: "dark red, dark gray, and bright red". This landing site would allow the Athena rover an opportunity to investigate all three materials within close proximity (the best place on Mars to do so). There are no high resolution (better than 100 m/pixel) Viking or Mariner images of this site. (2) Central Sinus Meridiani Region (proposed by K. S. Edgett and T. J. Parker) Central Sinus Meridiani is characterized by two types of surfaces [4]. One is like typical martian cratered highlands elsewhere- there are old valley networks and old impact craters. The other is relatively smooth and flat. These two units are in contact around 3.1 S between 5 W and 4 E longitudes. Valley networks- including one at 6'S, 358 W that rivals the Grand Canyon of Arizona- once drained toward the smooth unit. Edgett and Parker [4] proposed that the smooth unit might consist of sediments laid down in a large Noachian-aged sea/ocean that would have covered much of the northern hemisphere. Schultz and Lutz [I I I suggested that it is a paleopolar layered deposit. Regardless, the smooth unit where it contacts the cratered terrain would make an excellent site for Athena rover to investigate. The site is best seen in Viking high resolution images from orbits 408B (about 30 m/pixel) and 746A (about 12 m/pixel). These images suggest that aeolian deflation has occurred along the margin of the smooth unit, and this deflation has exposed horizontal larrs of material. The elevation is about 0.5 km; thermal inertias are 6.5-8.0 x 10(exp -3) cal /sq cm s(exp -0.5) / K; rock abundances are 2-4%; and the surface is probably sandy with dark drifts and ripples but almost no actual dunes. We suggest a landing around 3.2 S, 3.0 W would test the aqueous sediment hypothesis and provide a potentially smooth surface on which to land. (3) Amenthes Fossae Region (proposed by S. N. Huntwork and K. S. Edgett) The Amenthes Fossae are a series of graben/fissures that are circumferential to the southeast side of Isidis Planitia. These fissures cross a variety of ancient, heavily cratered Noachian terrain and younger, Hesperian and Amazonian terrain. We focused our search on a region 0-15 N, 250 - 270 W. Elevations are -0.5 to 2 km. Depending upon whether Isidis Planitia was ever a water-rich environment, this region might have been influenced by aqueous sedimentation. Valley networks are common, and they drained toward the north and northwest. We focused our work on a set of Viking orbiter high-resolution images, 719A 1-48. These have resolutions 16-24 rri/pixel. We examined images 20-23, centered at 2 N, 258 W. This site, on the plains just southwest of a 42 km-diameter crater, includes a valley network channel, a relatively young crater ejecta deposit, a few buttes composed of presumably ancient, Noachian bedrock, and a "plains" unit. The plains might make an ideal landing surface, except for the presence of some fine-scale ridges (oriented approximately N-S). The ridges are probably yardangs, thus this site offers a place where aeolian deflation has probably exposed some of the layered rock units that comprise the "plains". Thermal inertias are 7.9-8.3 x 10(exp -3) cal/sq cm s(exp -0.5) /K and rock abundances are 10-15%. A rover traverse might include the opportunity to go down to the floor (and sample along the walls) of the valley network channel at 2 N 258.1 W.

Edgett, K. S.↗

NASA NTRS2022

Brain Aging Hallmarks: A Primer for Future Studies on Space Radiation Effects

As humankind endeavors to travel farther away from Earth, many questions remain to be solved to ensure proper preparation for deep space. Multiple spaceflight stressors can elicit adverse health outcomes including exposure to space radiation. Space radiation exposure has been identified by the National Aeronautics and Space Administration (NASA) as an important contributor to cancer, degenerative tissue diseases including cataracts, cardiovascular disease, immune system dysfunction and possible central nervous system decrements. The complexity of the human central nervous system makes it difficult to adequately recapitulate in experimental model systems, which hinders quantitative description of associated decrements. The brain aging hallmarks, as introduced by Mattson and Arumugam in 2018, are measurable cellular and molecular hallmarks that generally contribute to the aging process, describe an aging phenotype, and are part of the etiology of age-related neurodegenerative diseases. These hallmarks include mitochondrial dysfunction, accumulation of oxidatively damaged molecules (oxidative stress), impaired lysosome and proteasome function, dysregulation of neuronal calcium homeostasis, compromised adaptive cellular stress response, aberrant neuronal network activity, impaired deoxyribonucleic acid (DNA) repair, inflammation, impaired neurogenesis and dysregulated energy metabolism. Cellular senescence and telomere attrition may also be considered, though more evidence is needed to regard them as brain-specific hallmarks of aging. Radiation exposure has previously been correlated with aging etiology; therefore, investigating the effects of radiation exposure within the context of the hallmarks of brain aging may provide insights into potential health risks facing NASA astronauts, and may provide a means to identify disease processes that may be important targets for disease prevention or intervention. This work describes the hallmarks of brain aging and serves as a primer for future investigation into how the hallmarks of brain aging may compare and contrast with outcomes associated with exposure to the space radiation environment. Further, it will be useful in future identification of hallmarks that may be appropriate to target for radiation countermeasures specific to the central nervous system.

Vivian Lu↗

DOE OSTI2023

Quantum Key Distribution for Critical Infrastructures: Towards Cyber-Physical Security for Hydropower and Dams

Hydropower facilities are often remotely monitored or controlled from a centralized remote control room. Additionally, major component manufacturers monitor the performance of installed components, increasingly via public communication infrastructures. While these communications enable efficiencies and increased reliability, they also expand the cyber-attack surface. Communications may use the internet to remote control a facility’s control systems, or it may involve sending control commands over a network from a control room to a machine. The content could be encrypted and decrypted using a public key to protect the communicated information. These cryptographic encoding and decoding schemes become vulnerable as more advances are made in computer technologies, such as quantum computing. In contrast, quantum key distribution (QKD) and other quantum cryptographic protocols are not based upon a computational problem, and offer an alternative to symmetric cryptography in some scenarios. Although the underlying mechanism of quantum cryptogrpahic protocols such as QKD ensure that any attempt by an adversary to observe the quantum part of the protocol will result in a detectable signature as an increased error rate, potentially even preventing key generation, it serves as a warning for further investigation. In QKD, when the error rate is low enough and enough photons have been detected, a shared private key can be generated known only to the sender and receiver. We describe how this novel technology and its several modalities could benefit the critical infrastructures of dams or hydropower facilities. The presented discussions may be viewed as a precursor to a quantum cybersecurity roadmap for the identification of relevant threats and mitigation.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1997

Buckets, Clusters and Dienst

In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

Nelson, Michael L.↗

NASA NTRS2004

A Multi-Discipline, Multi-Genre Digital Library for Research and Education

We describe NCSTRL+, a unified, canonical digital library for educational and scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 100 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets". We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information.

Nelson, Michael L.↗

DOE OSTI2020

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. Here, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.

59 BASIC BIOLOGICAL SCIENCES↗